| Kota Kasahara, Hideyuki Tsuboi, Michihisa Koyama, Akira Endou, Momoji Kubo, Calros Adriel Del Carpio, *Akira Miyamoto |
"Tight-Binding Quantum Chemical Molecular Dynamics Study on First Proton Transfer Process of ORR Catalyzed by Cobalt-Porphyrin Complex." |
2006 |
Electrochemical and Solid State Letters |
9 |
A490-A493 |
doi: 10.1149/1.2336985 |
URL |
| *Kota Kasahara, Kengo Kinoshita, Toshihisa Takagi |
"Ligand-binding site prediction of proteins based on known fragment-fragment interactions." |
2010 |
Bioinformatics |
26(12) |
1493-1499 |
doi: 10.1093/bioinformatics/btq232 |
PubMed |
URL |
| *Takeshi Obayashi, Kozo Nishida, Kota Kasahara, Kengo Kinoshita |
"ATTED-II updates: condition-specific gene coexpression to extend coexpression analyses and applications to a broad range of flowering plants." |
2011 |
Plant and Cell Physiology |
52 |
213-219 |
doi: 10.1093/pcp/pcq203 |
PubMed |
URL |
| Kota Kasahara, Matsuyuki Shirota, *Kengo Kinoshita |
"Comprehensive classification and diversity assessment of atomic contacts in protein-small ligand interactions." |
2013 |
Journal of Chemical Information and Modeling |
53(1) |
241-248 |
doi: 10.1021/ci300377f |
PubMed |
URL |
| Kota Kasahara, Matsuyuki Shirota, *Kengo Kinoshita |
"Ion Concentration-Dependent Ion Conduction Mechanism of a Voltage-Sensitive Potassium Channel." |
2013 |
PLoS ONE |
8:e56342 |
1-8 |
doi: 10.1371/journal.pone.0056342 |
PubMed |
URL |
| Kota Kasahara, *Kengo Kinoshita |
"GIANT: pattern analysis of molecular interactions in 3D structures of protein–small ligand complexes." |
2014 |
BMC Bioinformatics |
15:12 |
1-6 |
doi: 10.1186/1471-2105-15-12 |
PubMed |
URL |
| Bhaskar Dasgupta, Kota Kasahara, Narutoshi Kamiya, Haruki Nakamura, *Akira R Kinjo |
"ATTED-II updates: condition-specific gene coexpression to extend coexpression analyses and applications to a broad range of flowering plants." |
2014 |
PLoS ONE |
9:e91347 |
1-16 |
do+I6i: 10.1371/journal.pone.0091347 |
PubMed |
URL |
| *Kota Kasahara, Ikuo Fukuda, Haruki Nakamura |
"A Novel Approach of Dynamic Cross Correlation Analysis on Molecular Dynamics Simulations and Its Application to Ets1 Dimer-DNA Complex." |
2014 |
PLoS ONE |
9(11):e112419 |
1-13 |
doi: 10.1371/journal.pone.0112419 |
PubMed |
URL |
| *Junichi Higo, Bhaskar Dasgupta, Tadaaki Mashimo, Kota Kasahara, Yoshifumi Fukunishi, Haruki Nakamura |
"Virtual-system-coupled adaptive umbrella sampling to compute free-energy landscape for flexible molecular docking." |
2015 |
Journal of Computational Chemistry |
36(20) |
1489-1501 |
doi: 10.1002/jcc.23948 |
PubMed |
URL |
| Kota Kasahara, Matsuyuki Shirota, *Kengo Kinoshita |
"Ion Concentration- and Voltage-Dependent Push and Pull Mechanisms of Potassium Channel Ion Conduction" |
2016 |
PLoS ONE |
11:e0150716 |
1-15 |
doi: 10.1371/journal.pone.0150716 |
PubMed |
URL |
| *Kota Kasahara, Neetha Mohan, Ikuo Fukuda, Haruki Nakamura |
"mDCC_tools: characterizing multi-modal atomic motions in molecular dynamics trajectories" |
2016 |
Bioinformatics |
32(16) |
2531-2533 |
doi: 10.1093/bioinformatics/btw129 |
PubMed |
URL |
| *Kota Kasahara, Kengo Kinoshita |
"Landscape of protein-small ligand binding modes." |
2016 |
Protein Science |
25(9) |
1659-1671 |
doi: 10.1002/pro.2971 |
PubMed |
URL |
| *Kota Kasahara, Benson Ma, Kota Goto, Bhaskar Dasgupta, Junichi Higo, Ikuo Fukuda, Tadaaki Mashimo, Yutaka Akiyama, Haruki Nakamura |
"myPresto/omegagene: a GPU-accelerated molecular dynamics simulator tailored for enhanced conformational sampling methods with a non-Ewald electrostatic scheme" |
2016 |
Biophysics and Physicobiology |
13 |
209-216 |
doi: 10.2142/biophysico.13.0_209 |
PubMed |
URL |
| *Kota Kasahara, Kengo Kinoshita |
"IBiSA_tools: A Computational Toolkit for Ion-binding State Analysis in Molecular Dynamics Trajectories of Ion Channels " |
2016 |
PLoS ONE |
11(12): e0167524 |
1-9 |
doi: 10.1371/journal.pone.0167524 |
PubMed |
URL |
| Hasitha Muthumala Waidyasooriya, Masanori Hariyama, Kota Kasahara |
"An FPGA Accelerator for Molecular Dynamics Simulation Using OpenCL" |
2017 |
International Journal of Networked and Distributed Computing |
5(1) |
52-61 |
doi: 10.1109/ICIS.2016.7550743 |
URL |
| *Junichi Higo, Kota Kasahara, Bhaskar Dasgupta, Haruki Nakamura |
"Enhancement of canonical sampling by virtual-state transitions" |
2017 |
The Journal of Chemical Physics |
146: 044104 |
1-12 |
doi: 10.1063/1.4974087 |
PubMed |
URL |
| *Kota Kasahara, Masaaki Shiina, Ikuo Fukuda, Kazuhiro Ogata, Haruki Nakamura |
"Molecular mechanisms of cooperative binding of transcription factors Runx1–CBFβ–Ets1 on the TCRα gene enhancer." |
2017 |
PLoS ONE |
12(2): e0172654 |
1-18 |
doi:10.1371/journal.pone.0172654 |
PubMed |
URL |
| Hasitha Muthumala Waidyasooriya, Masanori Hariyama, Kota Kasahara |
"OpenCL-Based Implementation of an FPGA Accelerator for Molecular Dynamics Simulation." |
2017 |
Information Engineering Express |
3(2) |
11-23 |
|
URL |
| *Junichi Higo, Kota Kasahara, Haruki Nakamura |
"Multi-dimensional virtual system introduced to enhance canonical sampling." |
2017 |
The Journal of Chemical Physics |
147: 134102 |
1-13 |
doi: 10.1063/1.4986129 |
PubMed |
URL |
| *Kota Kasahara, Shun Sakuraba, Ikuo Fukuda |
"Enhanced Sampling of Molecular Dynamics Simulations of a Polyalanine Octapeptide: Effects of the Periodic Boundary Conditions on Peptide Conformation" |
2018 |
The Journal of Physical Chemistry B |
122(9) |
2495-2503 |
doi: 10.1021/acs.jpcb.7b10830 |
PubMed |
URL |
| *†Kota Kasahara, *†Masaaki Shiina, Junichi Higo, Kazuhiro Ogata, Haruki Nakamura |
"Phosphorylation of an intrinsically disordered region of Ets1 shifts a multi-modal interaction ensemble to an auto-inhibitory state." |
2018 |
Nucleic Acids Research |
46(5) |
2243-2251 |
doi: 10.1093/nar/gkx1297 |
PubMed |
URL |
| †Naoki Ogasawara, *†Kota Kasahara, Ryosuke Iwai, Takuya Takahashi |
"Unfolding of α-helical 20-residue poly-glutamic acid analyzed by multiple runs of canonical molecular dynamics simulations" |
2018 |
PeerJ |
6:e4769 |
1-17 |
doi: 10.7717/peerj.4769 |
PubMed |
URL |
| Tomonori Hayami, Kota Kasahara, Haruki Nakamura, *Junichi Higo |
"Molecular Dynamics Coupled with a Virtual System for Effective Conformational Sampling" |
2018 |
Journal of Computational Chemistry |
39(19) |
1291-1299 |
doi: 10.1002/jcc.25196 |
PubMed |
URL |
| †Ryosuke Iwai, *†Kota Kasahara, Takuya Takahashi |
"Influence of various parameters in the replica-exchange molecular dynamics method: Number of replicas, replica-exchange frequency, and thermostat coupling time constant" |
2018 |
Biophysics and Physicobiology |
15 |
165-172 |
doi: 10.2142/biophysico.15.0_165 |
PubMed |
URL |
| *Kota Kasahara, Shintaro Minami, Yasunori Aizawa |
"Characteristics of interactions at protein segments without non-local intramolecular contacts in the Protein Data Bank" |
2018 |
PLoS ONE |
13(12): e0205052. |
1-14 |
doi: 10.1371/journal.pone.0205052 |
PubMed |
URL |
| Shinji Iida, Takeshi Kawabata, Kota Kasahara, Haruki Nakamura, *Junichi Higo |
"Multimodal Structural Distribution of the p53 C-Terminal Domain upon Binding to S100B via a Generalized Ensemble Method: From Disorder to Extradisorder" |
2019 |
Journal of Chemical Theory and Computation |
15(4) |
2597-2607 |
doi: 10.1021/acs.jctc.8b01042 |
PubMed |
URL |
| *Kota Kasahara, Hiroki Terazawa, Takuya Takahashi, Junichi Higo |
"Studies on molecular dynamics of intrinsically disordered proteins and their fuzzy complexes: A mini-review" |
2019 |
Computational and Structural Biotechnology Journal |
17 |
712-720 |
doi: 10.1016/j.csbj.2019.06.009 |
PubMed |
URL |
| Tomonori Hayami, Junichi Higo, Haruki Nakamura, *Kota Kasahara |
"Multidimensional virtual-system coupled canonical molecular dynamics to compute free-energy landscapes of peptide multimer assembly" |
2019 |
Journal of Computational Chemistry |
40(28) |
2453-2463 |
doi: 10.1002/jcc.26020 |
PubMed |
URL |
| Yusuke Nomoto, Yukihiro Kubota, Yuto Ohnishi, Kota Kasahara, Aimi Tomita, Takehiro Oshime, Hiroki Yamashita, Muhamad Fahmi, *Masahiro Ito |
"Gene Cascade Finder: A tool for identification of gene cascades and its application in Caenorhabditis elegans" |
2019 |
PLoS ONE |
14(9):e0215187 |
1–16 |
doi: 10.1371/journal.pone.0215187 |
PubMed |
URL |
| †Takuya Shimato, *†Kota Kasahara, Junichi Higo, Takuya Takahashi |
"Effects of number of parallel runs and frequency of bias-strength replacement in generalized ensemble molecular dynamics simulations." |
2019 |
PeerJ Physical Chemistry |
1:e4 |
1–20 |
doi: 10.7717/peerj-pchem.4 |
URL |
| *Junichi Higo, Kota Kasahara, Mitsuhito Wada, Bhaskar Dasgupta, Narutoshi Kamiya, Tomonori Hayami, Ikuo Fukuda, Yoshifumi Fukunishi, *Haruki Nakamura |
"Free-energy landscape of molecular interactions between endothelin 1 and human endothelin type B receptor: Fly-casting mechanism" |
2019 |
Protein Engineering, Design and Selection |
32(7) |
297–308 |
doi: 10.1093/protein/gzz029 |
PubMed |
URL |
| *Kota Kasahara, Yuki Takimoto, Ryoi Ashida, Takuya Takahashi |
"Effects of ion–water Lennard-Jones potentials on the hydration dynamics around a monovalent atomic ion in molecular dynamics simulations." |
2020 |
Molecular Simulation |
46(2) |
83-91 |
doi: 10.1080/08927022.2019.1675883 |
URL |
| *Masatake Sugita, Masataka Hamano, Kota Kasahara, Takeshi Kikuchi, Fumio Hirata |
"New Protocol for Predicting the Ligand-Binding Site and Mode Based on the 3D-RISM/KH Theory" |
2020 |
Journal of Chemical Theory and Computation |
16(4) |
2864–2876 |
doi: 10.1021/acs.jctc.9b01069 |
PubMed |
URL |
| *Junichi Higo, Takeshi Kawabata, Ayumi Kusaka, Kota Kasahara, Narutoshi Kamiya, Ikuo Fukuda, Kentaro Mori, Yutaka Hata, Yoshifumi Fukunishi, Haruki Nakamura |
"Molecular interaction mechanism of a 14-3-3 protein with a phosphorylated peptide elucidated by enhanced conformational sampling" |
2020 |
Journal of Chemical Information and Modeling |
60(10) |
4767-4880 |
doi: 10.1021/acs.jcim.0c00551 |
PubMed |
URL |
| *Kota Kasahara, Hiroki Terazawa, Hayato Itaya, Satoshi Goto, Haruki Nakamura, Takuya Takahashi, Junichi Higo |
"myPresto/omegagene 2020: a molecular dynamics simulation engine for virtual-system coupled sampling" |
2020 |
Biophysics and Physicobiology |
17 |
140-146 |
doi: 10.2142/biophysico.BSJ-2020013 |
PubMed |
URL |
| *Junichi Higo, Ayumi Kusaka, Kota Kasahara, Narutoshi Kamiya, Itaya Hayato, Xie Qilin, Takuya Takahashi, Ikuo Fukuda, Kentaro Mori, Yutaka Hata, Yoshifumi Fukunishi |
"GA-guided mD-VcMD: A genetic-algorithm-guided method for multi-dimensional virtual-system coupled molecular dynamics" |
2020 |
Biophysics and Physicobiology |
17 |
161-176 |
doi: 10.2142/biophysico.BSJ-2020008 |
PubMed |
URL |
| Tomonori Hayami, Narutoshi Kamiya, *Kota Kasahara, Takeshi Kawabata, Jun-ichi Kurita, Yoshifumi Fukunishi, Yoshifumi Nishimura, Haruki Nakamura, *Junichi Higo |
"Difference of binding modes among three ligands to a receptor mSin3B corresponding to their inhibitory activities" |
2021 |
Scientific Reports |
11 |
6178 |
doi: 10.21203/rs.3.rs-139177 |
PubMed |
URL |
| Hayato Itaya, *Kota Kasahara, Qilin Xie, Yoshiaki Yano, Katsumi Matsuzaki, Takuya Takahashi |
"All-Atom Molecular Dynamics Elucidating Molecular Mechanisms of Single-Transmembrane Model Peptide Dimerization in a Lipid Bilayer" |
2021 |
ACS Omega |
6(17) |
11458–11465 |
doi: 10.1021/acsomega.1c00482 |
PubMed |
URL |
| *Shun Sakuraba, Qilin Xie, Kota Kasahara, Junichi Iwakiri, Hidetoshi Kono |
"Extended ensemble simulations of a SARS-CoV-2 nsp1-5'-UTR complex" |
2022 |
PLoS Computational Biology |
18(1) |
e1009804 |
doi: 10.1371/journal.pcbi.1009804 |
PubMed |
URL |
| Ryohei Kondo, *Kota Kasahara, Takuya Takahashi |
"Information quantity for secondary structure propensities of protein subsequences in the Protein Data Bank" |
2022 |
Biophysics and Physicobiology |
|
e190002 |
doi: 10.2142/biophysico.bppb-v19.0002 |
URL |
